Merge pull request #462 from catalystneuro/add_one_photon_series

Refactor `add_two_photon_series` to `add_photon_series` and add support for `OnePhotonSeries`

Author: CodyCBakerPhD

CHANGELOG.md

@@ -48,6 +48,9 @@
 * Added basic temporal alignment methods to the AudioInterface. `align_starting_time` is split into `align_starting_times` (list of times, one per audio file) and `align_global_starting_time` (shift all by a scalar amount). `align_by_interpolation` and other timestamp-based approaches is not yet implemented for this interface. [PR #402](https://github.com/catalystneuro/neuroconv/pull/402)
 * Changed the order of recording properties extraction in `NeuroscopeRecordingInterface` and `NeuroScopeLFPInterface` to make them consistent with each other [PR #466](https://github.com/catalystneuro/neuroconv/pull/466)
 * The `ScanImageImagingInterface` has been updated to read metadata from more recent versions of ScanImage [PR #457](https://github.com/catalystneuro/neuroconv/pull/457)
+* Refactored `add_two_photon_series()` to `add_photon_series()` and added `photon_series_type` optional argument which can be either `"OnePhotonSeries"` or `"TwoPhotonSeries"`.
+  Changed `get_default_ophys_metadata()` to add `Device` and `ImagingPlane` metadata which are both used by imaging and segmentation.
+  Added `photon_series_type` to `get_nwb_imaging_metadata()` to fill metadata for `OnePhotonSeries` or `TwoPhotonSeries`. [PR #462](https://github.com/catalystneuro/neuroconv/pull/462)
 
 ### Testing
 * The tests for `automatic_dandi_upload` now follow up-to-date DANDI validation rules for file name conventions. [PR #310](https://github.com/catalystneuro/neuroconv/pull/310)

requirements-minimal.txt

@@ -1,12 +1,10 @@
-numpy>=1.22.0,<1.24;python_version<'3.11'
-numpy>=1.22.0;python_version>='3.11'
+numpy>=1.22.0
 jsonschema>=3.2.0
 PyYAML>=5.4
 scipy>=1.4.1
 h5py>=2.10.0
 hdmf>=3.4.7
-pynwb>=1.4.0;python_version>='3.8'
-pynwb>=1.4.0,<2.3.2;python_version>='3.11'
+pynwb==2.3.2;python_version>='3.8'
 psutil>=5.8.0
 tqdm>=4.60.0
 dandi>=0.46.2

src/neuroconv/schemas/metadata_schema.json

@@ -248,6 +248,19 @@
               "imaging_plane": {"type": "string"}
             }
           }
+        },
+        "OnePhotonSeries": {
+          "type": "array",
+          "items": {
+            "title": "OnePhotonSeries",
+            "type": "object",
+            "required": ["name", "description"],
+            "properties": {
+              "name": {"type": "string", "default": "OnePhotonSeries"},
+              "description": {"type": "string"},
+              "imaging_plane": {"type": "string"}
+            }
+          }
         }
       }
     }

src/neuroconv/tools/roiextractors/__init__.py

@@ -3,9 +3,9 @@
     add_fluorescence_traces,
     add_image_segmentation,
     add_imaging_plane,
+    add_photon_series,
     add_plane_segmentation,
     add_summary_images,
-    add_two_photon_series,
     check_if_imaging_fits_into_memory,
     get_nwb_imaging_metadata,
     get_nwb_segmentation_metadata,